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ProteomicsLimited proteolysis for PTM analysis
PTMs on a mycobacterial DNA-binding protein with a long, lysine-rich, intrinsically disorders region were analyzed by limited proteolysis with trypsin, unveiling a massive methylation of most lysine residues of the protein in quantitative manner, which was lacked in the recombinant version of the pr...
ORGANISM(S): Escherichia Coli Mycobacterium Tuberculosis Mycolicibacterium Smegmatis Mc2 155 
2024-06-14 | PXD042969 | JPOST Repository
ProteomicsLarge-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins using Limited Proteolysis
Conformational changes in proteins can lead to disease. Thus, methods for identifying conformational changes in proteins can further improve our understanding and facilitate detection of disease states. Here we combine limited proteolysis (LiP) with Stable Isotope Labeling with Amino Acids in Cell ...
ORGANISM(S): Homo sapiens (Human) 
2016-12-23 | PXD005210 | Pride
Proteomics Limited proteolysis Mass spectrometry Silac Mcf-10a Mcf-7 Protein folding 
ProteomicsA map of protein-metabolite interactions reveals principles of chemical communication
Application of a novel mass spectrometry-based high-throughput workflow (LiP-SMap) and data resource based on limited proteolysis (LiP) of complex samples. Proteome-wide limited proteolysis sites were obtained in different conditions to infer ligand-induced and protein-protein interaction induced co...
ORGANISM(S): Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2018-01-04 | PXD006543 | Pride
Small molecules Limited proteolysis Lip-smap Dia-ms E.coli 
ProteomicsFLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe
Here, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as a method that can provide proteome-wid...
ORGANISM(S): Bacillus cereus (strain ATCC 14579 / DSM 31) 
2024-05-24 | PXD047776 | Pride
Data processing Proteomics Limited proteolysis Bacillus cereus atcc 14579 Bacilli Mass spectrometry Bioinformatics Bottom-up Data 
ProteomicsLarge-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins using Limited Proteolysis
Conformational changes in proteins can lead to disease. Thus, methods for identifying conformational changes in proteins can further improve our understanding and facilitate detection of disease states. Here we combine limited proteolysis (LiP) with Stable Isotope Labeling with Amino Acids in Cell ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080770 | MassIVE
ProteomicsCortisol binding sites on SARS-CoV-2 S1 identified by limited proteolysis-coupled mass spectrometry
We used a limited proteolysis-coupled mass spectrometry approach to pinpoint binding sites of cortisol on SARS-CoV-2 S1. Binding target identification is based on the principle that small-ligand binding alters (increases or decreases) the protease accessibility of the target protein37,38. The bindin...
ORGANISM(S): Severe acute respiratory syndrome coronavirus 2 
2022-06-10 | PXD032937 | Pride
Limited proteolysis Lc-ms Cortisol Covid-19 Sars-cov2 spike s1 
ProteomicsLimited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells
To study protein structures directly within cells, we developed in-cell limited proteolysis-coupled mass spectrometry (in-cell LiP-MS). Conditions for introduction of proteinase K into human cells using electroporation were optimized and validated for intracellular cleavages. In-cell LiP-MS captured...
ORGANISM(S): Homo sapiens (Human) 
2025-11-09 | PXD069095 | Pride
Stress granules Mass spectrometry In-cell lip Structural proteomics Limited proteolysis Arsenite treatment Rapamycin 
ProteomicsProteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.
Proteins regulate biological processes by changing their structure or abundance to accomplish a specific function. In response to any perturbation or stimulus, protein structure may be altered by a variety of molecular events, such as post translational modification, protein-protein interaction, agg...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-01-10 | PXD031627 | Pride
Alpha-synuclein Shotgun proteomics Yeast Structural proteomics Lip-ms 
ProteomicsBenchmarking of quantitative proteomics workflows for Limited proteolysis mass spectrometry
Limited proteolysis coupled with mass spectrometry (LiP-MS) has emerged as a powerful technique for detecting protein structural changes and drug-protein interactions on a proteome-wide scale. However, there is no consensus on the best quantitative proteomics workflow for analyzing LiP-MS data. In t...
ORGANISM(S): Homo sapiens (Human) 
2025-03-31 | PXD055927 | Pride
Dia Tmt Limited proteolysis Staurosporine 
ProteomicsLimited proteolysis of SARS-CoV-2 Spike treated at pH 2 or pH 7
SARS-CoV-2 is a respiratory virus spreading via aerosol particles. Aerosol particles can exhibit extreme environmental conditions affecting contained viruses, including acidic pH. Here, we study how harsh pH conditions, such as pH 2, can affect the structure of Spike, which is the main protein media...
ORGANISM(S): Homo sapiens (Human) Severe acute respiratory syndrome coronavirus 2 
2025-07-17 | PXD064612 | Pride
Sars-cov-2 Lc-ms Spike Acidic ph Lip 
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